FIG 5.
Mad-1 and WT3 bind to LSTc with higher affinity than gangliosides. (A) Example for the concentration-dependent crystal soaking experiment. The simulated annealing omit map contoured at 3.0 σ around 2.0 Å of LSTc at 2-4 Å resolution for JCPyV WT3 shows better defined features of the ligand with higher concentration. LSTc (yellow) is shown as a reference in all panels. Data from soaked crystals were scaled to a reference data set, and density around the Neu5Ac moiety was used for electron density integration. (B and C) Concentration-dependent crystal soaking experiments and electron density integration of Fobs − Fcalc simulated annealing omit maps within a 1.0-Å mask around Neu5Ac moieties of LSTc, GM1, GM2, GD1a, or GD1b within the conserved binding site of Mad-1 and WT3 VP1. Values for the electron density obtained by MAPMAN (53, 54) are plotted against the ligand concentration. Water molecules in the binding site contribute to the overall electron density of Neu5Ac when the occupancy is <1.0.